A fox of darkness, and the Fox of light
by jboy44
Summary: When Shinji is absorbed into Eva-01, he suddenly finds himself in the land of shinobi as the Jinchūriki of Kurama's evil Yin half. Found by Naruto, Shinji is brought to the Leaf as the fox tells Naruto of his family, leading to Naruto unlocking the Rinnegan! If Shinji thought being a pilot was hard, let's see how he handles being a shinobi!
1. Chapter 1

Shinji Ikari, the Third Child of NERV, recently absorbed into Eva-01, was in a black void when he saw his mother.

Shinji Ran to his mother crying.

His mother held him and told him, "Don't cry. I've never left you."

Shinji looked at her like he was about to say ask what she meant but she cut him off by saying, "My soul is what powers Eva-01. I'm trapped inside of it."

Shinji backed away crying, "THAT MONSTER IS MY MOTHER'S COFFIN!"

Yui got down and continued. "Your father betrayed me and all of humanity, son. He pushed me into this thing, knowing that it would absorb me to power itself. The same thing goes for all the other pilot's Eva's, except Rei since she's a clone of me. "

Shinji was crying more. "WHAT?!"

Yui sighed. "Your father wants the power that lies below NERV. The second Angel, Lilith. He also holds Adam, the father of the other Angels. He used this to draw the Angels who only want to save their father from NERV so that his Evangelion would be needed, but he didn't stop there. He plans on uniting and fusing with the first two Angels to absorb the souls of everyone on Earth to make himself a god, and he made you the way you are now to do it."

Shinji buried his hands in his face and cried. "I've been used by everyone, but used to bring about the end of the world?"

Yui kissed him on the head and said, "Son. You're inside Eva-01. It absorbed you, but since it only needs my soul, you will leave this place. But, I won't send you back to Gendo. I'll send you to a new world where people know how to use the A.T Field. There, you can lean what you need to stop him."

Shinji looked at her as he cried, "No! I don't want to be alone!"

Yui put a hand on his shoulder and told him, "You won't be alone. I've made sure of that."

Yui then disappeared as something that looked like the Grim Reaper appeared before Shinji and stabbed the boy in the gut, making a seal appear on his stomach making the boy black out.

Meanwhile, in another world…

Naruto was walking towards the Valley of the End, beaten and without Sasuke.

Suddenly, he saw Shinji in his school clothes out cold on the rocky ground.

Naruto bent over and threw the boy over his shoulder. "Just because I failed doesn't mean you have to die kid. What are you doing all the way out here, anyway?"

Inside Shinji's mind...

Shinji found himself walking through a sewer, asking, "How did I get here, and where is here?"

He kept walking, looking for a way out until he came to a gigantic cage that held a mountain-sized purple fox with nine tails and glowing red eyes.

Shinji quickly fell over and screamed at the sight.

The fox looked at him. "Greetings, mortal. I am the Yin half of the great Nine Tailed Demon Fox."

Shinji backed away after hearing the word 'demon.'

'If Angels were responsible for all of the evil I've seen, I don't want to see what a demon can do!'

The fox sat with his front hand-like paw's under its chin. "Boy, there is nowhere for you to go where I will not be, for this is your mind and I have been sealed within you by that overprotective mother of yours."

Shinji's eyes widened, "SAY WHAT?!"

The fox rolled his eyes. "In this world, what you know as the A.T Field is called chakra and everything you believe in your world is wrong. The only limits to what it can do is yourself, but back to the point. Here, those weakling Angels of yours never came. But, one demon did and it unleashed endless horrors onto the world until one man with the biggest balls in history discovered chakra and used it to seal the monster's soul inside himself, becoming the first Jinchūriki."

Shinji just sat there and nodded for the fox to continue.

The fox looked at him. "A Jinchūriki protects the world by keeping a demon trapped in their own body like a living jail. Now, this man, known as the Sage of Six Paths, knew with his death that the demon would be free again, so he sealed its body inside the moon and ripped its soul into nine pieces that became the nine Tailed Beasts. None of us hold a candle to the original demon's might."

The fox took a deep breath before continuing. "Nine families became the Jinchuuriki, passing us tailed beasts from one to the other, hoping that no one would find out that they were a Jinchūriki, because most of the time Jinchūriki are treat like weapons or the demons they guard. But, one day, 13 years ago, the second Jinchūriki of the Nine Tailed Fox died in child birth, forcing her husband to reseal it with in their newborn son and, to seal a Tailed Beast, you must die. Thus, the boy was left an orphan who was treated like it was the Nine Tails."

The fox then finished." And, when you die sealing a Tailed Beast, your soul is eaten by the Shinigami along with any souls sealed within you. So, the father took me, the Yin half of the Fox, with him and I rotted with in the Shinigami's stomach until that mother of yours, wanting to keep you safe, made a deal with the Shinigami to send you here with me sealed within you to keep you safe by healing all your wounds and giving you my power when needed for you to return one day to put an end to your father's evil. And now, we are in this together, no matter how much we hate it."

Shinji's eyes where wide, but want to show some spine for once. He stood up. He was shaking, but he was up and he said, "If we're in this together, then I should know your name right?"

The fox tilted its head and told him, "Boy, it's been a long time since anyone has asked a demon for their name, so in honor of that I will grant you the honor of knowing the name my good twin and I share. It's Kurama."

Shinji was still shaking but he asked, "So, Kurama… How do I get out of here?"

Yin Kurama responded, "By waking up from your coma."

Shinji just looked down.

Meanwhile, in the outside world…

Naruto made it to the gates of the village to see Sakura who, right away, was mad about him not bringing back Sasuke and she yelled out, "I KNEW I SHOULDN'T HAVE PUT MY TRUST IN YOU, IDIOT!"

The Yang half of Kurama then said to Naruto, "Why do you care about this banshee? She hates you and even if you brought him back she wouldn't like you any better. Go ahead and ask."

Naruto not knowing why he was going to listen to the demon that made his life hell, he asked Sakura the question. "What would have happened if I did bring him back for you?"

Sakura shut up for a second before thinking that he must want to know what could have been. "Simple, dummy. It all would have went back to normal. Nothing would have changed. I would have Sasuke and you would still be the dummy pointlessly asking me out. But, I guess him not coming back is my own fault for believing in you."

Naruto made a fist and growled angrily about the demon being right but his eyes remained blue. However, now a faint, almost invisible ring formed in his eyes as he said, "I guess you're right about me being an idiot after all. I wasted way too much time chasing after you."

He then walked past her and informed told her, "Now if you please in need to get this kid I found on the way back to a doctor."

Before he could make it to the hospital, Root ANBU appeared, knocked him out and grabbed Sakura.

Within Naruto's mind…

Naruto found himself in front of the fox's cage.

"This is the end. That mad man Danzo has made his move to overthrow this village and he's going to try to remove me from you and, just to make this clear, when a demon is removed from someone, the human we leave dies. So, if he gets me, you die, just like what happened with your mother," Yang Kurama suddenly informed him.

Naruto was freaking out. "I CAN'T BE HOKAGE IF I'M DEAD…! Wait… My mother…?"

Yang Kurama rolled his eyes. " Well, since you're going to die, you might as well know. Your mother was Kushina Uzumaki, my second Jinchūriki. You see now, you Uzumaki have been protecting the world from me by sealing me within your bodies for years now. My first Jinchūriki was the wife of the first Hokage. But, back to Kushina. She was your mother. When she first found out she was pregnant, she was the happiest woman on the planet. I know. I had to put up with the joy and mood swings from within her mind for 9 months."

The demon fox shivered from the memory before continuing. "But, on the night she gave birth in a hidden location, someone found her and killed her, unleashing me. That's how I appeared out of nowhere. But, I wasn't attacking this place. I was trying to get the feeling back in my legs when you all attacked me. Then the fourth, who, believe it or not, was your father, had to seal me away into you because only an Uzumaki can contain the Nine Tailed Demon Fox and not die. But, before he was eaten by the Shinigami, he took my Yin half with me, making me nothing but Yang, or good."

Naruto looked dumbfounded, but, before the whole 'the Fourth is his father' thing sank in, he said, "If you're the good half, I don't want to see the evil half."

Yang Kurama growled. "Hey! By demonic standards, I'm a saint! If I wasn't I wouldn't point out the shadow clones of themselves your parents made to be sealed in you if anything went wrong so that you could meet them. They are sealed in the wall behind you."

Naruto turned around to see a wall with the words mother and father written in kanji on it.

"Ok. How the hell did I miss that?"

Yang Kurama sat with his hands under his chin. "You're always focused on me when you come here. Not what's around me. But, go ahead. Touch them. See what happens."

Naruto touched the symbols and, sure enough Kushina Uzumaki and Minato Namikaze appeared and both hugged Naruto.

Naruto was being hugged by his parents. His thoughts raced.

'My dad was the fourth. The third had to have known, just like granny Tsunade and the pervy sage. Did they not tell me to protect me or was it something else?'

A second almost invisible ring formed in his eyes.

Naruto cried. 'I could have had parents, a family and the respect of this village if one man hadn't done this.'

A third almost invisible ring formed in his eye.

Suddenly, Kushina asked him, "Naruto. How's your twin sister?"

As Naruto cried, he took on a shocked expression. He asked, "Sister?"

His parents then gasped, Kushina was in tears. After all, if your son didn't know he had a twin sister, then something horrible had to have happened. No one saw the fourth almost invisible ring form in Naruto's tear filled eyes.

Yang Kurama spoke up. "You two need to know about your son's life."

He then showed the two their son's life. Both became angry and their eyes became full of tears.

Kushina's hair split, making it look like she had nine tails and she yelled at Minato "I TOLD YOU WE SHOULDN'T HAVE MADE YOUR PERVERT OF A TEACHER HIS GODFATHER! HE NEVER CAME ONCE TO TAKE CARE OF HIM! HE'S EVEN MORE OF A GOOD-FOR-NOTHING THAN EVEN I BELIEVED!"

Seeing that Kushina was angry, Kurama retreated into his cage and muttered, "Glad I'm safe in my cage… Sucks to be a Namikaze male right now…"

Meanwhile, in a room in the Root base…

Shinji was waking up in a holding cell only to look through the bars an ANBU – or as he saw it, a man in a uniform – was talking to a one-armed, one-eyed man who was called Danzo – not that he knew his name yet.

The Root ANBU spoke, "As shocking as it sounds, this boy has the yin half of the fox sealed within him, and it looks like it was just sealed in him today, Lord Danzo."

Danzo smirked. "Then I seems that luck is on our side regarding the fact that its evil was too much for the Shinigami to hold in. We shall kill him and the Namikaze brat and I shall use my implanted Sharingan to contain both halves of the beast so that I may use its complete power."

Shinji just gasped then quickly covered his mouth as the two looked his way.

Danzo eyed Shinji. "You had a Tailed Beast sealed inside of you just hours ago, yet you are already awake. Such potential… It's a shame it will have to be wasted for me to gain ultimate power."

Danzo then left.

"My memories from the time I was one with my good twin tell me that man is Danzo an evil man who stops at nothing to get power," Yin Kurama informed Shinji.

Shinji looked down at his hands to see a band on his right arm.

"Great. Another version of my father. What's this band?"

"First, I can hear your thoughts, so don't reply to me aloud. People will think you're crazy. Second, it's a chakra sealing band. As long as it's on you, you can't use chakra or, as you call it in your world, the A.T field. But, there's a way around that. You see, my chakra can overload it and the pure power my demonic chakra has should be enough to get you out of here. The only problem is that I sense a drug in your system that stops you from getting angry and, without anger or rage, you can't call upon my power," Yin Kurama responded.

Shinji tucked his legs into his chest, wrapped his arms around him and replied to the fox aloud, "So I'm screwed six ways to Sunday."

Yin Kurama let out an evil chuckle and stated, "Not if you overload the drug with your emotions of this long buried memory."

Flashback…

A four year old Shinji was getting a hug from his mom.

Yui kissed him on the head before walking over to Eva-01.

"Don't worry, Shinji. Mama will be right back."

She then climbed into Eva-01 as Gendo smirked evilly. Yui never came out.

End flash back…

Shinji was crying as he growled, "I was there… He trapped my mother in that monster and made me watch…" The band on his arm started to crack as he growled. "Gendo…"

The Root ANBU who stood guard looked back to see the boy's eyes change to match the demon sealed within him. He ran off quickly to warn Danzo.

Yin Kurama kept putting the image of Gendo's evil smirk into Shinji's mind, saying, "He killed your mother for power. He used you to try to become a god. He killed your mother and put you in her coffin. He killed your mother. Took her from you when you were just a child. He killed your mother who, for who knows why, loved him. He killed your mother and ruined your life. He killed your mother and used her soul to power a manmade demon. He killed your mother, used her face on a clone to try to control you. He killed your mother. He killed your mother. Your father killed your mother. He killed your mother."

The band on Shinji's arm shattered into dust as a one tailed fox chakra shroud made of purple chakra formed around him and he yelled out, "GENDO! I'LL KILL YOU!"

Shinji then rammed down the door by just running at it. He ran through the Root hallways with one thought on his mind. 'Must escape and kill Gendo.'

Meanwhile…

Naruto woke chained to a table to see Danzo. Right away, Naruto asked, "What happened to my sister?"

Danzo smirked. "I see Minato must have sealed a Shadow Clone of himself in the seal as well. Well, I don't see the harm in telling you, seeing as the chains that hold you will block all chakra within your body from being used. I kidnapped her at birth and sold her to Orochimaru. Her name was Karin."

Naruto growled. He kidnapped and sold his sister like a slave to Orochimaru.

Danzo then left, leaving only two Root guards as 2 more rings that could almost not be seen formed in Naruto's eyes.

Naruto growled as he thought to himself, 'Danzo cost me my sister. The Sharingan has cost me my whole family.'

A sixth ring formed in his eye as he thought, 'Sasuke and my whole family are gone thanks to those stupid evil eyes…'

Naruto's eyes then changed. All six rings became as clear as day and his eyes took on a grayish color. In short, Naruto had unlocked the Rinnegan, making his half of Kurama gasp out, "My father's eyes?!"

Naruto tried to get free as he yelled, "Orochimaru! Danzo! The Uchiha! They cost me everything! I'll kill all of you!"

His guards, having no emotions, did not react or look back to see his new eyes.

Yang Kurama spoke to him. "You have the eyes of my father… From my time within my father's body, with my brothers and sisters I saw through his eyes how to use them… So, in honor of my father, I give you the knowledge of how to use your eyes."

Naruto remained still for a moment before saying, "Preta Path, Chakra Absorption."

He took Chakra from emotionless guards and, using that power, he broke his chains, freeing his own.

Naruto walked to the door and pushed his hand forwards as he stated, "Shinra Tensei."

An unseen force then pushed the door to the ground as Naruto walked out to find Danzo.

Yin Kurama then said to him, "I know you're pissed and are out blood, but Danzo is a smart one. He must have your friends trapped somewhere here. Save them, then kill the old fart so he has no one to use as a human shield."

Naruto sighed. "You're right, but I can't use Shadow Clones. I haven't trained to handle seeing out of six eyes yet. I'll have to do this without shadow clones. I never thought a day like this would come…"

To be continued…


	2. battle for the leaf round one

Naruto had knocked out a Root ANBU and placed his hand on their head.

"Human Path: Absorption Soul Technique," he spoke.

He began to read his mind and, having found out where the exit was and where the villagers were being held, he ran off.

Naruto thought to himself, 'I'll have to ask Tsunade to reveal my Jinchūriki status and my family. I also have a plan to prove that we are not one in the same, Nine Tails.'

The fox demon simply told him, "I have a name. It's Kurama."

Naruto paid the fox no mind as he quickly came to the door of the large holding cell the villagers were being held in. "Danzo's so sure of himself he didn't post a guard. Bansho Ten'in."

The door flew off its hinges as Naruto broke a chakra suppressing seal. The entire village saw Naruto's Rinnegan eyes.

Meanwhile…

At the other end of the base, Shinji was still in his purple one-tailed chakra shroud, running around like an animal looking for a way out.

Shinji was growling when he came to a dead. "STUPID MAZES! I HATE THEM!"

The chakra shroud grew slightly stronger which lead to Yin Kurama saying, "Then, why not just brake through it your wearing my power as armor? Nothing can stand in your way, kid."

Shinji then punched the wall, destroying it with his demonic chakra-powered fist.

Shinji looked at his hand as he thought, 'This is like an Evangelion going berserk, but in reverse.'

Yin Kurama thought to himself, 'The boy can't think while one and a half of my tails being used. His mind is stronger than that Gendo bastard, though. '

Shinji just continued running on all fours through the Root base, trying to find a way out.

Meanwhile…

Naruto had led the villagers to the exit and, as they left, he grabbed Tsunade by her wrist and said, "Tsunade, I know who my parents are. Tell the villagers – shinobi and civilian alike – who they were and what is sealed inside of me. Don't worry. I have a plan to show them that the Nine Tails and I aren't one in the same."

Tsunade was still in shock about Naruto's eyes, but just nodded as he let her go.

Yang Kurama then told Naruto, "Kit. My other half is in the base. I can sense him. Come to think of it, I sensed him in that kid you found. I guess the reaper couldn't take his evil anymore and threw him up."

Tsunade looked at Naruto and stated, "Come on, kid."

Naruto just shook his head. "I can't, Baa-Chan. The fox in me is just the good half of the Nine Tails and it told me that the evil half is down here. I've got to take care of that." He then vanished.

Tsunade's eyes widened. 'Wait… The Nine Tails that attacked us had a good side and the pure evil side is down here? I need a drink now more than ever…'

Naruto had vanished and was deep inside the Root base, walking through holes in the walls. "Smashed straight through. I like this kid's style."

Naruto then saw Shinji in a two tailed purple chakra shroud. The boy quickly jumped at Naruto. Naruto simply held his hand out and said, "Preta Path: Blocking Technique Absorption Seal."

Shinji's two-tailed Yin chakra shroud was then ripped form him and absorbed into Naruto, making the boy fall down onto his butt.

Shinji rubbed his head as he looked at Naruto and jumped a little. "Dude… What's up with your eyes and what the hell's going on?"

Naruto put his right hand on Shinji's forehead. "Let me just show you the Human Path's mind connection."

Shinji and Naruto then lived each other's memories like they were their own.

Naruto quickly took his hand off Shinji's head. "So… You're not from this world… I thought my life was weird…"

Shinji got off the floor. "No. Your life is way weirder, Naruto. Believe it!" Shinji then covered his mouth.

Naruto raised an eyebrow, "I think connecting our minds like that gave us some of each other's personality traits. Believe it!"

Yin Kurama thought to himself, 'This boy's broken mind isn't just remembering the holder of my father's mind's memories. It's fixing itself by treating them like they are his own. This boy will soon have this Naruto boy's 'always-get-back-up' attitude, plus the experience and knowledge of all of his jutsu. It's like some kind of shinobi cheat sheet. '

Naruto looked at Shinji before he turned around and told him, "Since you have had no shinobi training, I'll take you to the exit before I go after Danzo."

Shinji nodded as he followed Naruto to the exit.

Once they came to the exit, Shinji parted ways with Naruto and headed up the stairs to the village, only stopping once as a flashback hit him.

Flashback…

Shinji was standing in front of Mizuki when he used shadow clone.

End flashback…

Shinji shook his head. "What the -? That was one of Naruto's memories. It had to be. So, why was I seeing it through his eyes?"

Yin Kurama smirked. "Your mind is so broken thanks to your father's work that it's trying to fix itself by copying that Naruto boy's. So, kit. Looks like you have his experience when it comes to jutsu. That's what you call the use of chakra, or, as you know it, the A.T field."

Shinji just started to walk up the stairs again as his mind flashed back to Naruto learning the basics of chakra use and control. "This is giving me a headache."

Meanwhile…

Naruto came to the door leading to Danzo's office, knowing full well that the old war hawk would be in there getting ready to try to remove the Nine Tails, quickly moved his hand forwards and said, "Shinra Tensei."

The door fell in, making Danzo turn to see the Rinnegan in Naruto's eyes. The war hawk quickly uncovered the Sharingan eye in his head and pulled out his ten Sharingan arm that had the face of the first Hokage on its shoulder. "The Rinnegan. The eyes of a god. Child, you are full of surprises. I must have them at once."

Danzo slammed his hands on the ground. "Wood Release: Tree Bind Flourishing Burial."

A giant tree started to form around Naruto.

Naruto quickly used the Preta Path to make a dome around himself. The tree grew around him. He wasn't tied up, but he was still trapped inside of the tree.

Naruto quickly closed his eyes and made a Shadow Clone and, without opening either of their eyes, they charged and made one really big Rasengan. He dropped the dome and Naruto and his clone pushed the Giant Rasengan into the tree, making a hole big enough for him to get out.

The Shadow Clone dispelled itself and Naruto jumped out to Danzo's shock.

Naruto formed an incomplete Rasengan in both hands and charged at Danzo saying, "Don't underestimate me."

Danzo pulled out a kunai and charged it with wind charka to make it a full-sided sword. "I won't. Wind Release: Vacuum Blade."

He held his wind sword out and used it to hold back to two Rasengan, forcing Naruto to jump back and dispel them.

Danzo looked at the boy. "He's had the eyes of a god for under an hour and has already learned how to use them to their fullest. If the teachers at the academy had bothered to teach you right, no doubt you would have been top of your class. But, with those eyes being what made the Sharingan, all 11 of my eyes are useless against you. No part of it would dare under estimate you, boy."

Danzo quickly slammed his hand to the tree around him. Then, he went up. He was using the tree like an elevator to get to the village and, once there, Danzo made the tree open only to see that the shinobi were free and defeating his Root ANBU. "The boy has ruined my master plan. Damn him. Well, I guess the apple doesn't fall far from the tree."

Back in Danzo's office, Naruto removed his jacket, took out a knife and quickly cut his own wrist. "Don't heal this, Kurama. I'm going to use the Animal Path to summon you and I want us both to bleed to prove we are not one in the same."

Naruto saw that the cut wasn't healing. "Good." He did the hand signs for the summoning jutsu. "Animal Path: Summoning jutsu. Yang Kurama, the Nine Tailed Fox." He then slammed his hands on the ground making smoke cover the room.

Up in the village, the Nine Tailed Fox, Kurama, with the Rinnegan in his eyes and a bleeding right paw popped out of the ground with a bleeding Naruto on its head.

Danzo's eyes widened. "Of course. The Rinnegan made the Tailed Beasts. It would allow you to summon and control one."

Naruto just smirked. The sight of both the Nine Tails and himself bleeding was enough to prove to the villagers he and the Nine Tails where not one in the same, making all of them feel sickened for the way they treated him and become fearful of the revenge he could unleash upon them with the Tailed Beast under his power and with the Rinnegan.

Danzo growled. "You are a bigger thorn in my side than your father ever was, boy."

Naruto smiled. "Thanks. Now, Kurama. If you would be so kind as to finish this bastard off."

The Nine Tails smiled as it thrust it's claw through Danzo's chest, only for him to vanish.

Danzo appeared in front of Naruto and cut the boy across the chest with his wind sword.

Naruto held his bleeding chest as he fell off of Kurama and saw that one of the Sharingan in Danzo's arm was gone. "How?"

Danzo smirked. "Izanagi. A jutsu only usable though the Sharingan. The Sharingan transforms death into a genjutsu by altering space time, effectively giving the user another life at the cost of one Sharingan eye, and, as I have ten more of them, you would have to kill me 11 more times to be done with me."

Naruto dispelled Kurama so that he could return to the seal and start healing him as he said, "That's cheating."

Meanwhile…

Shinji just made it out of the root base and in to the forest where the exit brought him , when a Root ANBU with sword in hand jumped at him.

Without thinking, Shinji used the fox hand sign and said, "Shadow clone jutsu."

A clone of himself then appeared before him. However, it was quickly cut in half by the Root Agent's sword, making it go poof.

Shinji just looked at himself, shocked but grateful. 'Naruto, if I see you again, I'll need to thank you.'

Without thinking, he quickly formed an incomplete Rasengan in his hand and rammed it into the Root ninja's gut, sending them flying back into a tree.

Shinji blinked a couple of times. "I can freak out about this later. Right now, I'll try not to die." Five more Root shinobi appeared.

Shinji gulped as all five drew their blades. "Can we just talk about this?"

All five sword-wielding Root shinobi ran at him and, out of reflex, Shinji made hand sign. Then, as the Root ninja were about to all slash at him, Shinji switched places with one of them, making four Root agents kill their teammate.

Shinji backed away, scared. "Look. I'm sorry. I didn't know what I was doing. I didn't mean to kill your teammate."

Root shinobi one pulled his sword from the fallen Root shinobi. "He was a loser. Simple as that. Died to complete his mission and, unlike you, we of Root feel no emotions to weaken us."

Root ANBU two pulled his blade out as well. "You are clearly a civilian, yet you were able to pull off 3 jutsu, two of which are high ranking in power. Even without emotions, we must admit you have skill."

Roof ANBU three pulled his sword out of his fallen teammate as well. "We underestimated you simply because you had no shinobi headband. A mistake we won't make twice, boy."

The final Root ANBU pulled their sword free of the new Root ANBU corpse. "For we are Root. Making sure Danzo gets the power of the complete Nine Tails is our mission and we will complete it at all costs."

Shinji's eye's widened. 'What kind of cold-hearted monsters are they?'

Yin Kurama quickly replied with, "The same kind as your father, Gendo, who, in the name of power, killed your mother."

Shinji's eye's turned blood red as his pupils became slitted like a fox's. His teeth became fang-like and his nails became claw-like.

Root ANBU one spoke. "He is tapping into the Yin half of the fox's chakra. Plan Beta."

All four Root ANBU then ran around Shinji so fast that he couldn't keep up. All he knew was they were using their swords to draw something on the ground.

That something turned out of be a four-pointed star and all four Root shinobi stabbed their blades into the ground on which a point was drawn and yelled, "Four Star Restraint Seal!"

The star on the ground then glowed white as white glowing chains came out of the ground and wrapped around Shinji, forcing him down to his knees with his arms trapped at his sides, unable to break free.

Root shinobi number two let go of his sword as he watched Shinji struggling to get free. "Your struggling is pointless. This seal will hold you where you are now, unable to move your arms to use jutsu until lord Danzo comes to remove the Yin half of the fox from you, which will kill you."

Root shinobi three also let go of his sword's handle as he saw that Shinji was still struggling. "Trying, even when you have no hope to finish your mission, to escape Danzo. You would have made a fine shinobi, kid."

Shinji growled as purple chakra stormed around him, thinking, 'I can't die here. If I do, then I will never get home. I'll never see Misato again. Why is she the first one I think about? No. Stop it, Shinji. Now isn't the time for that. Get mad, damn it! The madder you are, the more of the demons power you gain.'

Shinji became to think about everything bad that had happened to him and how it was all Gendo's fault. This made him enter the one-tailed chakra shroud.

The first tail wasn't enough to break free, so he thought about the good things he had. Misato, his friends, Toji and Kensuke, and how, if he died here in this world, he would never see them again. This made his anger grow, making him enter the two-tailed shroud.

This still wasn't enough to break the chains, so he thought about Naruto's life. All the crap he was put through by the villagers and how he didn't want any payback and, instead, wanted to protect them. The boy had to be some kind of saint, to not be evil after all the hate he went through. Thinking about this led to Shinji entering the three-tailed shroud, making a mini hurricane form around him.

Shinji roared as he lifted his arms and the chains started to give, allowing him to move his arms up an inch away from his side, and he kept on fighting.

Root ANBU number one grabbed his sword's handle. "We have underestimated the kid once again. He's drawing in more of the Yin Nine Tails' power."

Shinji finally was able to push his right hand forwards, sending a chakra arm out that knocked one of the sword blades out of the ground, breaking the seal and making the chains vanish.

The four Root ninja grabbed their blades and quickly charged at him, but Shinji swung his claws forward, leaving four deep gashes in the chests of two of them and making them fall down and bleed out.

The last two didn't get any better as the chakra tails hit them in the head so hard that it broke their skulls, making the two fall to the ground, dead.

Shinji then passed out as his chakra shroud left him. He had used way too much chakra on the first go round.

As soon as he was unconscious, Shinji found himself in front of the fox cage and he yelled out, "I HOPE YOU'RE HAPPY! I'M A MURDERER, THANKS TO YOU!"

The fox chuckled. "Boy, in this world, everyone uses what you know as the A.T field for battle. Death in battle is a normal thing. Besides, you acted in self-defense. The courts in your world won't charge you for murder. Plus, you feel bad about it. A true killer feels no grief for the ones they killed. It was no different than what you made the Evangelion do on a regular basis. After all, they are just clones of the Angels."

Shinji bit his lip. The fox had a point. He did feel grief, so he clearly wasn't a monster, and he did make the Evangelion kill other Angels before. He was no different from the demon locked up before him, and that sucked.

Shinji looked down and made a tight fist. "No. I don't care. You may have piloted me into killing my own kind, like I do my Eva-01, but other than that, we are nothing alike, demon. I fight to keep others safe. You just want to kill!"

Yin Kurama smirked. "Your mother wanted me to help you get a backbone and grow a set. Well, we got some backbone, now. Let's work on the growing a set part."

To be continued…


	3. BFTL end, Striking a nerv

Naruto lay on the ground, clutching his bleeding chest with his right hand as he held his left arm out to Danzo who was currently coming closer. "Go, Naraka Path."

The King of Hell's head then popped out of the ground surrounded by black flames. It opened its mouth and an arm-like part of its mouth grabbed Danzo's tongue.

Naruto felt grossed out. "Eww… This is one of the creepiest and gayest things I've ever seen…"

The King of Hell then said, "I am the King of Hell. By the power of the Naraka Path, you will answer the Rinnegan user's question truthfully, or I shall devour you."

Naruto staggered before removing his hand from his chest wound to see that the blood was dry. "Ok then, Danzo. Did you do anything to my family before my parents were expecting me and my sister? If so, what are the full details of it?"

Danzo chuckled. "Clever boy. Now I have to tell you. Very well. My first action against your family was in the third ninja war. It was nine months after Dan had died and Tsunade had just given birth to their child. How she could be a mother and fight the war? So, I took the child from his hospital bed and gave it to Dan's cousin in the Namikaze clan who knew nothing of where the child came from. I had the doctors tell Tsunade that her baby was stillborn. That child grew up to be your father, making you Tsunade's grandson and a Senju clan member."

The King of Hell said, "This is true." It then let go of Danzo's tongue and disappeared.

Naruto smirked. "You know, what luck! Tsunade heard that and is on her way here to help me kill you."

Danzo's eyes – even the ones in his arm – widened. "The worst part is that you have a 90% chance of being right about that with your luck."

Naruto threw down a smoke bomb and vanished behind it.

Naruto stood behind a building, quickly closed his eyes and made a Shadow Clone.

The clone ran back out to battle Danzo while the real one bit his thumb to do the Summoning jutsu hand signs.

Danzo turned around, held out his hand and released a vacuum blast of wind chakra, only for the clone to go poof.

The real one then stepped out with Gamatatsu and Gamakichi on his shoulders.

Naruto blew out his own wind chakra blast as Gamatatsu spat out oil and his brother spat out flames. All three blasts fused together into one giant stream of blazing oil that hit Danzo dead on.

The two toad brothers then dispelled themselves to go back home as Naruto turned around and jumped back just in time to avoid a strike form Danzo's Wind Release sword.

Naruto smirked. "You only have nine Sharingan left, Danzo."

Danzo growled as he summoned another tree below him to take him to the top of the Hokage Tower.

Meanwhile, in the village below…

Tsunade had truly overhead Danzo's words and was on her way, knocking out his root ANBU like they were nothing in her rampage to kill Danzo for taking her baby away from her.

At the same time, Sakura was hiding as the other rookies and Team Gai handled the Root ninja problem as she said to herself. "The Fourth's son, the Fifth's grandson, the last heir to Uzushiogakure and he has the Rinnegan. Why did I say no to him every time he asked me out?"

Lee looked at Sakura with shock as he kicked away a Root shinobi. "Sakura, all of that has nothing to do with who Naruto is. He is himself, always has been always will be. If you show interest for any of those things, you would be nothing more than a gold digger."

Then it hit Lee. Sakura had only asked out Sasuke so many times because of his name and, now that Naruto had found two more last names, she wanted him. Sakura was a gold digger and, like Naruto before him, he had been too blinded by her cuteness realize it. He growled as he focused more on Danzo's shinobi.

While all of this was going on, in another world, a woman named Misato was kicking a purple demon's head, saying, "GIVE HIM BACK, YOU MONSTER! GIVE SHINJI BACK, RIGHT NOW!"

Eva-01 remained locked in its restraints, unmoving and unchanging while, within its mind, Yui thought, "Now I know who cares about my son the most. I can use that in my plan to stop Gendo."

The ghostly woman then did her husbands interlocked finger pose as she thought, "She is acceptable."

Speaking of the Third child, he had just regained consciousness in the forest with five Dead Root ANBU around him.

He quickly jumped to his feet, slightly freaked, " Ok, so it wasn't a dream. I'm in a different world where everyone can use the A.T Field – which is called chakra here – to do superhuman things. I was sent here by my mother who's trapped in the Evangelion, and I have an evil demon living in my head."

Yin Kurama then added, "You forgot killing these Root bastards, the ninja civil war has broken out thanks to their leader's coup d'état and having someone else's memories in your head that lets you use the jutsu they know at a way lower level."

Shinji then replied aloud by yelling, "I DIDN'T FORGET! I CHOSE NOT TO LIST THEM!"

The fox them then respond by calling Shinji a pussy.

Shinji just rolled his eyes as he walked away from the smell of the dead bodies around him. He didn't know where he was going, but anywhere had to be better than here, or, at least, that's what he thought.

Meanwhile, on top of the Hokage Tower…

Danzo was standing on top of the tower overlooking the war just as Naruto just made it to the roof. "Ok, Danzo. This ends now."

Yang Kurama then warned Naruto, "Kit, you have used a lot of chakra in this fight. I know I'm giving you more as you need it since you have my father's eyes, but still you're 12. Your body can't handle this much power. You need to be smart for once and either finish this off quickly or get him somewhere where you can have help."

Danzo smirked. "Boy, your courage is limitless, but your body's ability to handle the power you hold is not. Sooner or later, your body will burn out and you will die. I simply just have to outlast you and, seeing as I have ten more lives, that is an easy task. You have already lost, boy."

Naruto make his right arm glow. "Funny. That's what Neji said before I beat him."

Naruto held his glowing arm out towards Danzo as it transformed into a missile launcher that was loaded. "Asura Path: Rocket Launcher." The missile then fired as the parts of its launcher fell off Naruto's arm.

Danzo didn't move as the missile blew him up, only for him to reappear behind Naruto with only seven Sharingan left in his arm. "Like I said, being able to cheat death is a win."

Naruto turned to see Danzo coming out him with his wind sword, but Naruto stated, "Preta Path: Rasengan Dome."

A giant Rasengan then formed around Naruto, not only blocking Danzo's strike but also ripping the old man to shreds and sending his blood and guts everywhere.

Naruto dropped the dome and turned around to see Danzo reappearing five feet away from him with only six Sharingan left in his arm.

Danzo saw Naruto beginning to pant. "I will admit that outlasting you won't be as easy as I thought, seeing as I now only have six Sharingan left, but you are already starting to give out."

Naruto panted as he formed the Shadow Clone hand sign and said, "True, but I don't care if it overloads my senses. Multi Shadow Clone jutsu."

200 clones of Naruto then appeared but Naruto fainted as his first five clones dispelled, only leaving 195 clones.

The clones charged at Danzo only for him to begin cutting them down. "I see only you and your first five clones can use the Rinnegan because you share their senses. To see out of six sets of eyes is very useful data to have when I get those eyes for myself."

One of the clones was able to stab Danzo in the back of the neck, making Danzo fade away only to fade back into existence behind the clone with only five Sharingan left in his arm.

Danzo cut the clone in half as he said, "This is five times that you've killed me. Such power is wasted on you!"

Danzo began to cut through the clones once more just for the last one to stab him in the Sharingan he held in his right eye, sense he could not see through the Sharingan in his arm. This robbed him of the eye's genjutsu ability to copy jutsu, the ability to see what your opponent would do next and half his eyesight.

The clone then dispelled and the rush of his clone's memories forced Naruto back awake.

An enraged Danzo growled as he watched Naruto stumble back to his feet with a smug smirk on his face. "This ends now boy."

Danzo did some hand signs as he said, "Wood Release: Wood Dragon."

The tree Danzo used to get up to the top of the building then transformed into a dragon and raced at Naruto who could barely stand.

Naruto quickly did the summoning jutsu hand signs and spoke, "Animal Path: Summoning jutsu." Yang Kurama then appeared and slashed through the wooden dragon with its claws which, as luck would have it, also cut off Danzo's Sharingan arm, removing his ability to cheat death.

The fox then vanished as Naruto fell down to the ground, face first.

Danzo soon followed and collapsed from pain as he held the bleeding stub that was once his arm.

Naruto then said, "Your root ninja are losing Danzo. You no longer have the Sharingan. You will die from blood loss. It's over. You lose."

Naruto heard Danzo cursing as he blacked out.

Meanwhile…

Shinji found himself in the village as the last of the Root ninja where captured and found himself losing consciousness, just for the medical Shinobi to find him and rush him to the hospital.

Things in Leaf Village would never be the same again. For some, it would be worse. For others, it would be better. Danzo's evil was over, but this was just the beginning.

Naruto awoke in a hospital bed hours later, bandaged from head to toe with Tsunade standing over him, crying.

He spoke weakly. "What's wrong, Grandma?"

Tsunade pulled the boy in to a hug and cried. "The doctors did a DNA test. You are my grandson. I thought that I had no family left and I thought that I was going to lose you, too. That's what's wrong, brat."

Once Naruto was released from his grandmother's hug – something that he never would happen – he asked, "How's the village? Did you find the Shinji? He's the Jinchūriki of Kurama's evil half."

Tsunade wiped the tears from her eyes. "The village is fine. The elders want to force you into the Clan Restoration Act, but, as we're both Senju, they can't. After all, I know you didn't want to be a breading tool. And, yes we found him. The Yamanaka's went through his memories and showed us that that Evangelion thing is a real monster."

Naruto looked at her. She was clearly still freaked about his new eyes. "What about Karin, my sister? Are we going to go after Orochimaru to get her back?"

Tsunade cried again from the thought of her grandchild being in the snake's hands. "We're working on it, but everything is still in chaos. Just so you know, you're not alone anymore, Naruto. I'm your grandmother, Shizune – Dan's niece – is your cousin and we will find and save your sister."

Naruto had tears in his eyes. Today had been the worst day of his life, yet, he had what he had always dreamed about. Family. It was far too much for him to take in. "Grandma. Can I have some time by myself? This is just so much to take in at once."

Tsunade wasn't used to being called grandma, just as she was sure that Naruto wasn't used to having one, so she cried and said, "I will." She gave him a grandmotherly kiss on the head before she left, saying "The last thing you need to know is that no one hates you for having the Nine Tails."

Naruto just sat there and thought about his friends, mostly Hinata. He thought she was weird with all her blushing and fainting around him and her shyness. Then it finally hit him like a ton of bricks. "She as a crush on me and is too shy to talk to me, like some kind of reverse Sakura."

Reverse Sakura was the right choice of words. Hinata was shy and got to nervous to be around her crush, let alone ask him out, while Sakura was always around and trying to ask someone – mainly Sasuke – out.

Naruto remembered Sakura. "She never cared about me. If I hadn't been so blinded by that pink haired banshee's cuteness, I might have noticed sooner, I hope."

Naruto kept crying. A girl cared about him and he spent all the time chasing a girl who only wanted Sasuke, and, if she did want him now, it was only because of his name. Sakura only hurt him time and time again while Hinata always tried to help like when she gave him that healing ointment after his fight with Kiba.

Naruto hung his head low. "I know that seeing me chase after someone who didn't even like me must have hurt you Hinata, and I'm sorry. If you still like me in that way after all of this, I promise to make it up to you. Believe it."

And, in the doorway, one Hinata Hyuga was looking in with Tsunade behind her and the girl was crying tears of joy for the first time in her life.

On the other end of the hospital…

Shinji was awake in his hospital bed, looking up at the ceiling, "Waking up to another unfamiliar ceiling. Some things never change."

Jiraiya then walked in and said, "Hi, kid. You don't know me, but I'm Jiraiya the…"

Shinji cut him off by saying, "The super pervy sage."

Jiraiya had a tick mark on his head. "Of all the memories you could have gotten from Naruto, why did it have to be that one?"

Shinji looked up at the ceiling. "Let me guess. Since I need to be able to control my half of the Nine Tails, the people in charge of this place want you to train me and help me figure out a way back home?"

Jiraiya rolled his eyes. "Yes, and you are one big buzzkill, kid. You know that?"

Shinji nodded and said, "Yes. Do you know when I can get out of here?"

Jiraiya looked down. "In a couple of days, but you're being switched to a different room tomorrow, so just get some rest kid. You've been through the ringer like the rest of us have."

Shinji just nodded as Jiraiya turned to leave.

Meanwhile, in NERV…

It had been 2 hours and Misato and yet to stop kicking and screaming at Eva-01.

Ritsuko then walked up to her and pulled the angry woman away from the purple beast and said, "Misato, stop it. Shinji wasn't absorbed by it. The radiation signature inside its cockpit matches a previously theoretical wormhole."

Misato stopped kicking and turned around to face her friend before yelling out, "WHAT!?"

Ritsuko put her hand to her ears to try and stop the ringing. "The Evangelion didn't absorbed him. It sent him somewhere by bending space and time. He could be anywhere in space, time, or he may not even be in this universe anymore. The only one who has any clue where the Eva send him is Eva-01 itself."

Misato then quickly went back to kicking the thing's head yelling for it to bring Shinji back.

But, at that moment, in the other world, Shinji fell asleep and the eyes of Eva-01 came to life, scaring the shit out of Misato who quickly hid behind Ritsuko.

Maya was up at the controls, monitoring Eva-01 and, when she looked at the screen, she quickly hit the intercom button and screamed, "SHINJI'S MIND IS SYNCHING WITH EVA-1 AND HE'S NOT IN THE PLUG! WHAT THE HELL IS GOING ON?!"

In Shinji's mind…

He was sure he was dreaming. After all, he just fell asleep in a hospital in another world. Now he was back in NERV, inside the Evangelion.

Yin Kurama then told the boy, "I have no clue how it happened, boy, but when you fell asleep you, started synching with this manmade demon. You must have some kind of link to its mind."

Shinji tried to move the Evangelion's hand to its face to look at it, but found that he was restrained. All he could think was, 'A link between this monster's mind and my own? As if I didn't have enough demons in my head.

Maya once more screamed over the intercom, "A SECOND MIND IS SYNCHING WITH EVA-01! I'M SO SCARED! I THINK I WET MYSELF!"

Shinji then saw Misato hiding behind a shaking Rits, and Misato fearfully asked, "Sh-Shinji? Is that you?"

Shinji looked at her. He felt himself crying as he whispered her name to himself, but, sadly, as Evangelion couldn't speak the Eva did nothing but look at her before it shut back down. Whatever pulled Shinji's mind to the Eva had ended.

Misato was crying and shaking as Rits, quickly fainted as she wet herself.

Shinji found himself in his mindscape, crying and beating on a wall as yin Kurama looked on at how the sight of that Misato woman had brought the boy to tears.

Within the now-shut down Eva-01's mind, Yui was sitting on a beach with her fingers interlocked, thinking, "Shinji shouldn't have found out about or used the mind link to me – accidentally or not – this soon. This is going to be bad for the scenario."

Back in NERV…

Misato was forced to leave by the Ritsuko and her underlings so that they could figure out what just happened.

Misato got home to see Asuka, throwing out Shinji's stuff and moving her things in, making the girl scream, "WHAT ARE YOU DOING?!"

Asuka smiled. "Now that Shinji-baka is gone, I'm turning his room into storage. After all, he doesn't need it anymore."

Misato growled. "You go get Shinji's things, now. He'll be back. Just you watch."

Asuka sighed. "Misato, the idiot got himself killed. It's over. Move on. He's not coming back and, besides, I'm a way better pilot then he will ever be. We don't need him."

Misato then slapped the German girl across the face. "I wasn't asking what you think, you – you spoiled brat. Shinji will be back and, also, if you're our best pilot, we're all as good as dead, seeing as you're a throw-away. You never trained in the last year and just rushed into battle. I can't believe I ever stood up for you."

Asuka rubbed her face and walked away. "That's it. I'm going to Hikari's. You just cost yourself the honor of me living here, bitch."

She then left Misato's apartment.

Misato Sat down on her couch and listened to how quiet and lonely it was in her apartment now. "Why did I believe that she was a good kid? The others are right. She's just a red devil. Now I'm alone again. I mean, I still have Pen-Pen, but he's not much to talk to."

Pen-Pen then waddled out, holding a beer, and tried to hand it to Misato, but she said, "No thanks, Pen-Pen. I'm not in the mood for a drink."

Pen-pen dropped the beer and backed away slowly, scared for his life with a look of horror upon his avian face. After all, Misato not wanting beer had to be one of the signs that the end was near.

Misato got up and recovered Shinji's things which Asuka had thrown away and the first thing she saw was a cello. For the first time, she looked at it and its case only to see that the words 'Property of Yui Ikari. Please return if found' were written on the case.

Misato cried as it clicked. "I never saw Shinji play this because it's the last thing he has of his mom.'

To be continued…


	4. battle for the leaf aftermath part 1

Author's notes:

Jboy44: "Shinji is going to blend into the background a good bit in this chapter, but the next one will be all about him."

The next day, Shinji found himself moved into the same room as one Naruto Uzumaki Senju Namikaze.

Shinji looked over to Naruto who was sitting in his hospital bed with his arms crossed. "I guess they want us to be friends since we both have a half of the fuzz butt."

Naruto looked over to him and smirked. "Yes, and anyone who called the Nine Tails fuzz butt is ok in my book."

Meanwhile, in the hospital lobby…

The Fire Daimyo had just walked in, shocking everyone as he walked to the front desk.

The front desk lady was shocked as she nervously bowed and asked, "What can I do for you Daimyo-san?"

The Fire Daimyo stated, "I heard about what happened and I would like to check on one Naruto Uzumaki. After all, he is my younger sister Kushina's son."

The front desk lady froze for a second. Not only was Naruto the son of the Fourth, the last heir to Uzushiogakure and the Fifth's grandson, but he was related to the Daimyo, and after how she was always one of the people who hated the boy for having the nine tails in him, she just said, " room 203 first floor."

The lady then watched as the Fire Daimyo walked away as she thought, 'I'm so fucking dead! I was rude to a kid who's nobler than every last clan in the village!'

But, unknown to the lady and the Daimyo, one Hiashi Hyūga, who was just leaving from visiting Neji, had overheard and he placed his right hand on his chin as he thought, 'The boy is the rightful heir to the Namikaze, Senju, and Uzumaki clans and is the last heir of Whirlpool. Plus, he has the Daimyo for an uncle.'

He began to think as he put left hand under his right elbow. 'I don't hate the boy. I was a bit scared of the seal breaking because he wasn't a full blooded Uzumaki, but now that I know he's only half Uzumaki, that's not a problem. My daughter has feelings for the boy, and the elders want to put the Caged Bird Seal on her.'

The Hyūga then snapped his fingers as a plan came to his mind. 'I've got it. The elders won't seal Hinata if she is with someone as noble as the boy. She has feelings for him and, seeing as she cared about him before all of his heritage was revealed, just proving that will show him that she's the only one who has feelings for the real him.'

He then began to leave the hospital as he continued to think about the plan that was coming to his mind. 'The elder's won't seal her, seeing as that would bring the boy's wrath upon them. Plus, they would be too happy thinking about how a relationship between Hinata and the boy would make the Hyūga clan just as noble as the Daimyo.'

Hiashi smiled as he finished his train of thought. 'Hinata is happy to be with the boy, she doesn't get sealed, the elders don't have a problem with it and the boy gets the only girl who showed feelings for him before this big revelation. I won't have to seal one of my baby girls and everyone is happy. It's perfect. Now, I just need to figure out how to get Hinata to stop fainting around him.'

He then arrived home and headed towards the location of the elders, only stopping when he passed by Hinata and told her, "Hinata, if you end up with a relationship with the Uzumaki boy, you have my blessing."

Hinata just stood there in shock as she put her fingers together. "KAI!"

Hiashi looked back at her. "I understand why you did that." He then kept moving on towards the elders of his clan as Hinata fainted.

Back in Naruto and Shinji's hospital room…

Tsunade walked in and handed Naruto a map. "This is a map to your parent's house. The key is inside blood seal that only a Namikaze can open. You're moving in and, seeing as before the war every clan hid copies of their scrolls that held family histories, information on bloodline limits in the village and jutsu, in his library, you're going to find a lot of lost jutsu from different clans."

Naruto looked at the map and said, "Then I'll personally return the scrolls to the clans, Obaa-chan."

Tsunade then walked over Shinji. "Now, you need a place to stay."

Naruto then quickly said, "He can stay with me. After all, Jinchūriki have to stick together."

Tsunade smiled as she said, "You two are now healed, thanks to the fox. At 8 PM, you are both free to go and, Shinji, when you leave, a man named Iruka will be waiting in the lobby for you. Go to him and he'll take you to do the Genin test to see if just having some of Naruto's memories gives you the basics of being a shinobi."

Shinji just nodded along.

The fire Daimyo then walked in and said, "Lady Hokage, I hope I'm not interrupting anything, but…" He walked over to Naruto and removed his hat to reveal red hair, "My name is Kenshin Uzumaki, the Fire Daimyo, the older brother of Kushina Uzumaki, and thereby your uncle, Naruto."

Tsunade's eye's widened as Naruto just shrugged. "I used to think that I had no family. Now I have family coming out of the woodworks. I can believe it."

The Fire Daimyo then handed Naruto a pass. "This is proof of the right of free travel. A gift to you, my nephew. With this, you may leave the village and travel without the need of vacation time, a request or a mission. I give you this so that you may travel to find your sister and bring her home safely from the hands of Orochimaru. I will also give this right to anyone you wish to have it. Use it wisely."

Naruto, still sitting in his hospital bed, bowed to the man. "Thank you, uncle. I will do all in my power as holder of the Rinnegan to bring my sister back safely and make the snake pay for his crimes against our family."

The Fire Daimyo then put his hat back on. "That is all I ask. Now, Lady Hokage, come. I wish to speak to your council on the treatment of my nephew." He then left with a scared-as-hell Tsunade following him.

Naruto then put his fingers in the fox hand sign and said, "Shadow Clone jutsu."

One Shadow Clone of Naruto then appeared and both Naruto's put their hand on their head as the sensory overload of seeing what the other was seeing was still a little too much for him.

Shinji looked puzzled. "What are you doing?"

The clone and real Naruto then said, "I'm is trying to get use to the sensory overload as the Rinnegan makes the first five clones I make and myself of one mind and we see what each other see. While fighting Danzo, I only used clones twice. Once with my eyes closed to control only the clone and the other time I fainted from using as many clones as I could. Only the memories from the destroyed clones snapped me back awake, so I might as well train with this always active, controlling the power of up to six bodies before it gets me killed in the field."

Shinji just nodded. "That makes about as much sense as anything else that's happened in the last two days."

The real Naruto said, "If you want weird, try controlling two bodies at once while having them look at each other. It's like one of those infinite reflections is happening to your brain."

Shinji didn't know how to respond to that so he just stayed quiet.

The Naruto clone then left the room through the window and headed out into the village, only stopping when he saw his reflection in a window.

The clone looked at the battered, burned and dirty clothes he had on. "I'm going to need to get some new clothes, and hopefully with the last names of two Hokage and a Daimyo, the stores will sell me more than 'kill me' orange jumpsuits."

The real Naruto who was still in his hospital bed with his hand on his head and one hell of a headache stated, "Best head off to a store and see."

Shinji was watching. 'He's saying what his clone is, but he's not doing what the clone does. Is that good for controlling more than one body or bad?'

Yin Kurama then told Shinji, "It's good, seeing as it's how my father started with this ability."

The clone headed into a store and headed over to the cashier. "Sir, in the past you have overcharged me and only allowed me to buy orange. That ends now. Understand?"

The cashier nodded as he not only knew that how he treated Naruto was completely wrong, but all the ways he could end his life if he continued to treat him that way.

Naruto looked at him. "I know you own this clothing store and, as you have overcharged me for the last 12 years, I think it's only fair that anything that I buy here is half off for the next 12, don't you?"

Once more, the man nodded as he nervously as he sweated and said, "Yes, sir! I'm sorry! Don't kill me!"

Naruto walked over to some of the clothes. "You treated me like dirt and now that my last name has changed you want to kiss my ass. People like you make me sick, and you will pay for it, just like all the older generation of this village will. But, you won't pay with money or your lives. After all that would make me no better than you all."

The man gulped as he forced himself to ask, "Then, how will we pay you back, sir?"

Naruto looked him dead in the eye. "Simple. The truth will come out. Then my generation will lose all respect for yours and the one before you. Or, in short you will pay with the respect of your children, and the best part is that I won't and haven't done anything to make it happen."

Naruto then picked up a pair of black pants with a chain going from a belt loop to the right pocket, pair of black ninja shoes, an orange shirt and stated, "I believe that the store credit I have from you overcharging me is more than enough to pay for this."

The cashier then nodded as the Naruto clone folded the outfit under his arm and left for the hospital.

The clone, with Naruto's new cloths in hand, then re-entered and Shinji and Naruto's hospital room through the window he left through.

The clone walked over, put the cloths on Naruto's hospital bed, dispelled and Naruto fell backwards on to the bed as he held his head and let out a painful scream.

Shinji stupidly said, "At lest you stopped saying what your clone was saying after a while."

Meanwhile, in Misato's apartment…

It may have been a full day since he disappeared for him, but, in his home world, only 5 hour had passed and Misato was asleep on her couch, sweating a cold sweat as her sleep was filled with a nightmare.

In Misato's nightmare…

She was in a forest and she thought she spotted Shinji with his back turned to her, so she ran to him only for him to turn around to reveal a monster.

The monster was humanoid in shape with a layer of dark purple – almost black – energy covering its body. Atop its head were fox ears made from this energy. Four tails made from the same stuff were behind its back and it was solid black with two glowing, white, soulless, empty eyes. Misato didn't know it, but this was a Yin Release two-tailed chakra shroud.

A glowing ghostly white jagged line like a ghostly mouth was appearing on its face out of nowhere and it let out a roar as its hands grew large claws and swung at her.

That was when Misato awoke with a scream, panting and scared as she thought, 'If all dreams have a meaning, then what does that mean for Shinji?'

A another universe, in the Leaf…

Naruto had just come out of the hospital room that he shared with Shinji's bathroom in his new clothes. "I still feel like this outfit is missing something, but, right now, I have more important things to do. Shadow Clone jutsu."

A single clone of Naruto appeared, but, this time, neither held their heads from pain.

The real Naruto leaned against the wall as his clone left through the window. "Let's see how I can handle multitasking with the two bodies, now."

The real Naruto pulled out the map to his parents' house and read a note on it. "So, the Namikaze estate is hidden underground. No wonder the clans hid copies of their clan jutsu, training and history scrolls there in the third ninja war. After all, this place was pretty much levelled after the war. Who knows what lost jutsu I will find there."

Meanwhile…

The clone was walking around the village, seeing the villagers either ask for forgiveness, cry about how sorry they were or just stay away from fear. They still stared. "Great the only thing that changed is that they're now too chicken to attack me."

Out of the corner of his eye, he saw Hinata in Ino's family's flower shop, talking to Ino. So, he listened in to hear Ino say, "Did you hear, Hinata? The Fire Daimyo came to the village and revealed that he was Naruto's mom's older brother and he was mad at the villagers for not even listing his last name."

Hinata looked at her. "W-what do you mean, Ino?"

Ino, who was ringing up some flowers she was buying, told her, "In all the files the Daimyo saw, Naruto's last name wasn't listed. The council knew he was Naruto's nephew and stopped the Daimyo from knowing that his sister's son was alive."

Hinata was paying for the flowers as she spoke. "W-why?"

Ino then added, "Well, it turns out that Sakura's mom has a sit on the council and headed this little sting out of spite that the Fourth always said no when she asked him out. So, since the Fourth didn't go out with her, she ruined Naruto's life and made a member of the Daimyo's family's life hell. Enough proof of this was found that Sakura's mom was sentenced to death and killed by the Daimyo himself right in the council meeting."

Both the real Naruto and his clone's eyes widened.

Ino handed the flowers to Hinata. "Let me guess. These are for Naruto?"

Hinata blushed as she failed to form any words. Ino just said, "Hesitation is conformation."

Naruto's clone then walked in and said, "Well, I'm flattered, Hinata."

The two girls turned to see the Naruto clone. They were a little shocked, but the clone said, "I'm just a Shadow Clone. The real me is still in the hospital room, but, when a shadow clone dispels, the original gets all their memories. You're basically talking to the real me."

Hinata just blushed as Naruto walked over to her and said, "Hinata, I kind of figured out why you blush and faint around me so much. I'm sorry I didn't notice before." He rubbed the back of his head. "And, if you will think of me the same way after all of these big revelations, then I would like to try and make a relationship between us work."

Ino was wide eyed as Hinata forced herself to say, "I would like that."

Hinata's face was redder than ever and she was trying harder than ever to not faint as Naruto smiled and said, "Thanks. I can leave the hospital at 8. How about we meet for ramen then?"

Hinata nodded yes as she handed the 'get better soon' flowers to the clone before she fainted, thinking, 'Best day ever.'

The clone Naruto held on to the flowers and asked Ino, "So, how's Sakura taking this?"

Ino put her hand on her cheek as she used it to hold her head up. "We won't know for a while, because, when the ANBU went to tell her, they found this shrine in her room that showed she made her own religion around Sasuke. In short, she was bat shit crazy. My dad is in a hidden location removing all her memories that involve Sasuke right now to try and make the girl sane again."

Naruto looked down. Sure she turned him down and hurt him a lot but still no one should have to go through that. "I see."

Ino looked down. "Hey, she spent everyday since she was five running after Sasuke, so I doubt she'll have any memories past when she first saw Sasuke when we were five left. In short, she's probably going to be a five year old girl trapped in a 12 year olds body. They say that when it rains, it pours, and this village is in the middle of one hell of shit storm."

The Naruto clone just turned around. "I know, and I'd better get these flowers to the real me before they wilt. Make sure Hinata knows that our plans for a date wasn't just something she dreamed about when she comes to."

Ino responded, "Trust me, I will. After all, it's the first good thing to happen since duck butt left, and I love the new look."

The real Naruto and the clone smiled at what Ino called Sasuke. "Thanks."

Back in the hospital…

Shinji looked at him. "I take it that something good just happened to your second body?"

Naruto smiled. "You'd better believe it."

Shinji just looked at the clock to see that it was noon and he started to grab his hair with both hands. "Great. Another 8 hours until we can leave. I'm going to go crazy in here."

Naruto watched him as his clone returned with the 'get better soon' flowers that Hinata bought. "You need to learn how to relax, kid. I mean, a body-stealing, possibly half snake, mad scientist and gay freak has my sister and I'm not going nuts about it."

Shinji's eye's turned red as he looked at Naruto and yelled, "THAT'S BECAUSE YOU KNOW THAT HE WILL LEAVE HER ALIVE SO THAT HE CAN TRY TO USE HER AGAINST YOU!"

Naruto looked at Shinji and said, "Calm yourself. Don't let the demon control you, Shinji." He formed a Rasengan in each hand, ready for a fight.

Shinji took a deep breath, then let it out as his eyes returned to normal. "I'm calm. Put away the balls of pain, please."

Naruto dispelled the Rasengan in each hand. "Good. I didn't want to hurt you."

Shinji just crossed his legs and said, "Say, Naruto, last night, something happened and I started to see through Eva-01's eyes, or, as you may know it from my memories, the big purple monster."

Naruto looked at him. "It could have been a dream, or maybe you have a link to it. Who knows?"

Shinji put his hands in his lap and said, "That's what worries me. What if I take over the thing without knowing it and destroy part of Tokyo-3, or what if someone else pilots it and that allows them to control my body?"

Naruto looked at him. "But what if that link is your only way back? After all. it sent you here, so it makes sense that it could send you back and forth between our two worlds."

Shinji blinked a couple of times before saying, "I never thought of that."

Naruto looked at him. "Life is all about figuring things out. Sure, it may take some time to figure some stuff out, but, given time, the answers will come to us."

Shinji raised an eyebrow. "Ok. That sounds like something you would read in a fortune cookie."

Naruto shrugged. "I'm new to this whole sage thing. Cut me some slack."

Shinji turned away from him. "Ok, but I'm not going to let this whole brain-to-brain link between the monster and I go any time soon."

Meanwhile, in a hidden location…

Tsunade was standing in front of one Root shinobi named Sai who was tied to chair.

Tsunade held a journal up in front of him. "You are still loyal to Danzo after his death. Let's see if what we found in his journal will change that."

Tsunade to held the journal up so that he could read it and Sai read aloud. "Sai is progressing faster than his brother Shin and has more skill than him, as well. So, I'm opting to poison Shin slowly to make it look like he is dying of a virus to kill Sai's last emotional attachment so that I can make him the perfect Root shinobi and get rid of the deadweight."

Sai's eyes bugged out of his head as he read it over. He knew that it was Danzo's handwriting, so it wasn't a fake. This broke all of the training to kill off Sai's emotions and he cried as he screamed, "BASTARD!"

To be continued…


	5. battle for the leaf aftermath part 2

When the time finally came for Naruto and Shinji to leave the hospital, the two left the room.

Shinji spoke up. "I guess I'll go to the estate after my Genin test and wait for you to get back from your date."

Naruto looked at him. "Sounds right, but be warned Shinji. The life of a shinobi is a dangerous one."

The two then headed down the stairs to get to the lobby as Shinji said, "Yes, and so is the life of an Eva pilot."

Naruto responded as the two of them continued down the stairs. "Yes, but, if you're a shinobi, it really will be you getting hurt. Not some manmade demon whose pain you feel."

Shinji just paled a bit and gulped. "Good point."

They finally came to the lobby to see Iruka holding a sign that read 'Looking for Shinji Ikari.'

Naruto then left to go meet Hinata for ramen while Shinji walked over to Iruka and told him, "Shinji here, sir, but I don't want to go by the name Ikari anymore."

Iruka signalled for Shinji to follow him as they left the hospital. "Then, what do you want to be called?"

Shinji thought for a second. "I don't know. I would just rather not have a last name than go by Gendo's last name."

Iruka spoke as they arrived at the academy. "Ok, well, seeing as there's no way that you could pass the written test, your Genin test is going to be on jutsu and skills with shuriken and kunai knives."

Shinji nodded an "ok" as they walked out to the empty academy's training area.

Iruka pulled out five Shuriken and handed them to Shinji, then pointed to five targets. "Ok. This part is simple and has two parts. Rapid fire and accuracy. You will start by trying to hit all five targets and hitting each as close to the center as you can."

Shinji nodded in understanding as Iruka ordered, "Begin."

Shinji threw the shuriken. He hit all five targets, but they were way off from the center.

Iruka handed Shinji five more shuriken, "Ok. Now, just try to throw this at one target as fast as you can."

Shinji threw all five at once and they all hit the middle of the target, making Iruka say, "Your speed makes up for your lack of accuracy."

Shinji soon found out that the kunai version of the test was the same as a shuriken test and he got the same result.

Iruka pulled a folded piece of paper and a pen out of his right pocket and, as he unfolded it, he spoke. "Weapon's test is a C. Not good, but not bad either."

Iruka wrote the mark down on the paper and said, "Ok, now, jutsu first. Substitute."

Shinji tried to use the memories of Naruto in his head to make the hand signs, hoping that it would work, and, in a flash, a cloud of smoke covered him and, when the smoke was gone, one of the targets was in his place.

Iruka looked back to see all five targets, so he turned to the one in front of him and said, "Ok, Shinji. I can give you an A for Transformation, but not Substitution."

Iruka was about to write it down when one of the targets behind him turned into Shinji and said, "I think you mean an A for both."

Iruka jumped back, screamed and fell to the ground, panting as he held his racing heart. "Yes. A for both."

Iruka calmed his heartbeat and told him, "Ok. Now, Transformation, and no Sexy jutsu."

Something in Shinji made him snap his fingers and say, "Darn."

Shinji just put his hands together and stated, "Transform." With a cloud of smoke, Shinji turned into what looked like Misato in a red thong bikini. "Sexy jutsu: Bikini Style."

Iruka passed out with a nose bleed and the blood from his nose made the shape of an A.

Shinji returned to normal and smiled. "You said no sexy jutsu. Not no Sexy jutsu and Derived jutsu."

Iruka slowly came to, enough to hear that so he said, "Look underneath the underneath. I see."

Shinji then made the fox hand sign and said, "Shadow Clone." Two Shadow Clones of himself then appeared and said, "I know clones are part of this test."

Iruka got up and opened two pockets on his flak jacket. He pulled out a headband and a kunai holder. He handed both to Shinji. "Seeing as how you handle Root shinobi just fine, welcome to the ninja rank of Genin, Shinji of the Hidden Leaf."

Shinji put the headband on and asked, "So, now what?"

Iruka smiled. "I'm supposed to save Jiraiya some time and teach you the Tree Climbing jutsu and Water Walking jutsu."

Shinji put the kunai holder on his right leg and pulled one out. "I know. Mark how far I get with the knife."

To be continued…

Author's notes

Jboy44, "Shinji is now a shinobi of the Leaf. The next chapter will bring this story's first arc, the Battle for the Leaf, to a close, and start the Shinji, Shinobi of the Leaf/ Hunt for a Sister arc."


	6. HFASSSOTL part 1 Moving out

Gendo sat at his desk in his office in his signature pose speaking with the SEELE's.

SEELE one spoke out. "The Third Child is gone. What do we go now, Gendo?"

Gendo looked down before explaining. "We'll simply get Eva-03 back running. Bring in Eva-04 and Eva-05."

SEELE two asked this follow-up question. "What of pilots?"

Gendo adjusted his glasses as he spoke. "Eva-03 will retain its original pilot, Eva-04 will be piloted by Kensuke Aida and Eva-05 by Hikari Horaki. With those he calls his friends in danger, the Third will quickly reappear."

A voice from all of the SEELE screens then demanded, "MAKE IT SO!"

Meanwhile, a universe away in a village of ninjas named after a leaf…

It was night time. The stars were shining and the moon was full. An overall beautiful night.

In the streets of the village, one Naruto Uzumaki was walking Hinata Hyuga home from their date who was blushing brighter than the stars.

The date was pretty simple, like most first dates. They simply met for ramen, so neither dressed up.

Hinata had remained quiet throughout most of it but, while Naruto was with her, he saw something that he never thought he would see in his life. Someone who looked upon him and only saw him.

In the past, when someone looked at Naruto, they saw the Nine Tailed Fox, a dumbass and now either the son of the Fourth or the second coming of the Sage of Six Paths.

Naruto smiled as Hinata kept blushing as she looked at him. It was so new to him, having someone to only see him and not his eyes, family or the demon, let alone it being a beautiful lady who wanted to be in a relationship with him.

Naruto looked down at one of Hinata's hands and debated over it with himself if it was too soon to try to hold it or not. But, he chose to go for it.

Naruto grabbed on to Hinata's hand making the poor girl's face glow redder.

Hinata's mind was racing. She was on a date with Naruto, he was walking her home and was now holding her hand. It was a miracle that she didn't faint.

Naruto smiled as she watched the shy Hyūga princess muster up the courage to hold his hand back.

Soon, they came to the Hyūga estate where Naruto told her, "Hinata, I enjoyed my time with you. We'll have to do this again some time." Naruto followed this by kissing her on the cheek, making it so that Hinata could not fight it anymore. She fainted right into his arms.

Naruto held her bridle style as she brought her to her estate's doors. "I'm going to die from going in like this, but it'll be worth it to see the look on those emotionless Hyūga's faces."

Meanwhile, in the Hokage's tower…

Kakashi and Kurenai entered the office to see Tsunade and Yamato.

Kurenai bowed and asked, "Lady Hokage, why have you called us here?"

Tsunade crossed her arms and stated, "Fixing the mistakes the Third made in picking the teams. Kurenai, your team is all tracking. No battle skills. Too overly specialized to work right in the field. Kakashi, you only trained the Uchiha."

Both sensei were wide eyed and scared as she continued with, "Furthermore, Kurenai, you have not taught Hinata a thing, so you are too motherly to her to be a good teacher. So, as of right now, Hinata will take Sakura's place on Team Seven and Hinata's replacement on Team Eight will be a new Genin named Sai."

Kurenai made a tight fist and growled. She knew that Naruto wasn't the demon and that he was the Fourth's son and the Sage of the Six Paths' second coming. But, she still hated the boy for captivating Hinata's heart and not even giving her the time of day for so long.

Tsunade looked to Kakashi and said, "Hatake, as punishment for not following through with your teamwork, you are here by replaced as Team Seven's teacher for Yamato."

Kakashi's eye bugged out of his head.

"WHAT?!"

He then quickly went back to hiding his emotions

Tsunade looked down with a sigh. "You only taught one student, and, as such, you are also forbidden to take up another team. Shinji will take Sasuke's place on Team Seven. The final piece of business that we have to deal with is Sakura. She is now a five year old in a teen's body and scared with no family."

Kakashi was still hiding his emotions. "Yes?"

Tsunade put an evil smile on her face and told him, "She was your student, so she's your responsibility. So you are now her legal guardian and, as such, let me be the first to welcome you to parenthood, Kakashi, by saying that this means that you will no longer be allowed to own of look at your favorite orange book."

Kakashi's eye bugged out of his head as he cried, only to have Yamato rip an orange book from his hand, saying, "Can't do the time, don't do the crime."

Kakashi fell to his knees, yelling, "No!"

This sight made Kurenai and Tsunade laugh at the pervert's pain.

Tsunade covered her mouth as she tried and failed to control her laughter. Kurenai was rolling around on the ground, holding her side and crying from her laughter.

Later on, Naruto arrived at the Namikaze estate, covered in some blood, none of which was his, to see Shinji waiting.

Shinji looked at him and asked, "I don't want to even know, do I?"

Naruto bit his thumb and wiped the blood on the door witch made it unlock. "No, you don't, Shinji."

Naruto opened the door, the two steps in side and the first thing they saw was a very special room.

The right side was blue, the left side pink. Two cribs were placed in it. The pink side of the room had a dresser and a fox plush with a ribbon that said 'For mama's little princess.'

The blue side had a dresser as well and a toad plush that had a tag that said, 'For dads future kick butt ninja.'

In the middle of the room hung a banner that said 'Welcome home, Naruto and Karin'.

This room was the nursery meant for Naruto and his sister that, thanks to three evil men, went unused.

Naruto just fell to his knees and cried, and who wouldn't cry from the sight of the love his parents had for him and his stolen sister… that neither would never feel…

Shinji just stood there, not knowing what to say or do for his new friend.

Shinji lowed his eyes as he made a tight fist and thought, 'The evil of a human heart hurt us both and robbed us of our mothers, Naruto. I will be strong enough to control your Yin half Kurama and, when I do, no one else will feel this pain. BELIEVE IT!

Yin Kurama rolled his eyes as he told Shinji, "Fat chance boy!"

Throughout the night, Naruto and Shinji both used Shadow Clones to train, explore the estate, read everything in the library and deliver scrolls holding jutsu thought to have been lost in the last war to the clans of the village.

The Nara clans scroll held jutsu for transforming shadows in to solid tools, like blades. A Shadow-based version of Tailed Beast chakra arms and with a lot of skills that beasts know as familiar that act like Summon creatures.

The Inuzuka clan scroll held knowledge of a lost version of the Combination Transformation jutsu. The lost version had the ninken and human partner fuse into a human sized wolf man.

This lost jutsu – Combined Form jutsu – also told a tale of a lost clan history that stated that the Inuzuka were once werewolves that breed with humans, watering down their wolf blood and that if preformed for the first time under the light of a harvest moon, this jutsu would fully unlock their werewolf blood, allowing the Inuzuka to transform into a wolf man under the light of the moon.

The Akimichi clan scroll held a size change jutsu that allowed them to store fat cells in scrolls sealed inside of their skin. This jutsu allowed them to shrink, making themselves lighter for more speed or bigger for more power in strikes.

It also had a side effect of the user being skinny no matter what they eat and having the Calorie Control jutsu before storing from having virtually unlimited fat cells to work with.

The Hyūga's had the shame of finding that the Eight Trigrams has six versions for Hyūga's with the elements of fire, water, lighting, earth and wind.

The style they had taught everyone was the earth style trigrams which he figured from its fixed, rigid movements and upon investigation showed that only a handful of Hyūga's had an earth attribute.

This meant that Hyūga's like Hinata thought to be failures just simply weren't taught the right jutsu.

This humbled the clan a bit.

The Yamanaka Clan scroll held jutsu that could repair the human mind, getting rid of insanity and a jutsu called Mind Nightmare. It was a genjutsu that brought the targets greatest fear to life before their eyes.

As for the bug using Aburame clan, he didn't reveal what was in their scroll, choosing to see if it was real first.

Lastly, the biggest kick in the pains came from a scroll that held a jutsu to evolve the Sharingan to the Mangekyo Sharingan. The jutsu only worked for Uchiha who never strike to kill, meaning that, even if Sasuke got a hold of the scroll, his trying to kill Naruto would stop the jutsu form working.

All in all, it was safe to say that the village was far stronger than before and had a lot of studying to do.

But, right now, let's focus on the three Genin now of team eight who were heading for the Hokage tower.

Shinji now dressed in a simple white shirt, blue shinobi pants with a knife holder on his right thigh and black ninja sandals.

"Why did Baba-chan ask us here?"

Hinata shyly tapped her index fingers together and answered, "Remember the letter? We are here to meet our new sensei, Yamato, and get ready for a long-term mission."

Naruto had his hands behind his back as he added, "Hopefully to get my sister away from the snake gay freak queen."

Somewhere in the world, Orochimaru sneezed and became pissed off at a blonde haired boy.

Once in her office, Yamato bowed and introduced himself. "I am Yamato. I'm the best choice for your sensei as I am a clone of the First Hokage made by and left for dead by Orochimaru. I can't breed and I'm not as powerful. But I retain the first power of Tailed Beast control and can teach you, Naruto, wood release. The fact that I am a clone is a secret ranked higher than SS-rank."

The three Genin just stood there dumbfounded by their new sensei's introduction. But Shinji managed to say, "Holy freak show."

Tsunade rolled her eyes, "Anyway we have to leads on Orochimaru's location we want you to investigate them, as well as go to Uzushiogakure ancestral home of the Uzumaki clan to reclaim all Uzumaki property there. Anko and Jiraiya will join you."

Both Naruto and Shinji then yelled out, "WHAT DID WE DO TO PISS YOU OFF ENOUGH TO STICK US WITH THOSE TWO FREAKS FOR WHO KNOWS HOW LONG BABA-CHAN?!"

Tsunade had a tick mark on her head as she thought aloud, "Great. Baka's in stereo."

Hinata quickly grabbed Naruto's hand and pulled Naruto out before Tsunade killed him. Then Shinji came running after.

Once back out on the village streets, Shinji looked at Hinata who was still pulling still pulling Naruto along by his hand.

"Hinata. You can stop pulling Naruto along now."

Hinata then stopped dead in her tracks and blushed as she released Naruto's hand.

Naruto looked at her and thought aloud, "Hinata, your shyness is just too cute."

Naruto quickly covered his mouth as his eyes bugged out of his head when he realized what he just said.

Hinata thought, 'He thinks I'm cute.' Then, she fainted.

Naruto quickly caught her as he said, "Having a shy girlfriend is going to be troublesome… Wait… Did I just say that Hinata was my girlfriend?"

Hinata regained consciousness in time to hear Naruto call her his girlfriend and she fainted again.

Shinji looked at Hinata. "Form your memories, I know that Anko is like the anti-Hinata, so I guess she's along to try to un-shy Hinata."

Naruto looked at him and thought, 'Makes sense.'

Meanwhile, with Kakashi….

The copy ninja was tearfully throwing away his Make Out Paradise books by order of lady Hokage herself.

Gai then burst in with Lee and said, "I heard about you taking care of your former student, Kakashi. Your flames of youth burn bright."

Lee and Gai then screamed, "Youth!"

Just then, Sakura arrived and joined them.

Kakashi held his heart and thought, 'The three of them are here and one of them lives here now. What arm tingles when you're going to have a heart attack?'

To be continued….


	7. HFASSSOTL part 2 ruined home

Jboy44: "I just want to let you know that Eva-05 and up will be their Rebuild of Evangelion versions."

Out on the road, Naruto, Hinata, Shinji, Yamato, Anko and Jiraiya had arrived at the ruins of Uzushiogakure.

Naruto looked at the ruins of the once great village. He never know it before it's destruction, but it still felt like he was a child seeing the ruins of his home after it burned down. It was a truly horrible feeling.

Naruto made a tight fist and growled. The fact that how the village was destroyed and by who was lost to time only made him feel a deep rage.

Hinata saw this and grabbed hold of his hand to try and calm him down.

Shinji looked off towards the once great village, then to Naruto and only thought one thing. 'If this place had not been destroyed, how different would your life be?'

Jiraiya coughed to get everyone's attention before saying, "Now, let's move out and start looking around. Naruto, make a clone to go with each of us, seeing as only an Uzumaki can open anything here."

Naruto put his hands in the fox hand sign and created four shadow clones.

One clone went with Yamato who really blended into the background.

One went with Shinji, another with Jiraiya and the last one with Anko.

The real Naruto headed off to a place that was all but calling him. He had no idea where he was going within the ruined village, but he came upon a temple that was untouched by the destruction all around it.

Naruto moved closer to it, making a seal appear on the ground behind him as it deactivated. Naruto looked back at the seal and thought aloud, "A barrier seal. That's why this temple is untouched."

Naruto quickly shook it off and headed into the temple to see a statue of all nine Tailed Beasts stacked on top of one another like a totem pole from lowest to highest. It started at the bottom with the One Tail and ended with the Nine Tails at the top.

Before the statue was a simple-looking Khakkhara staff that was standing in a base of stone.

Upon the hole in the stone was a plaque that read, 'Here rests the staff of the Sage of the Six Paths. With this weapon, he was able to combine all of the natural releases of chakra to use all hybrid elements. Only the rightful heir to his title and power may free this staff from the stone. All who are unworthy of the being the heir of the Sage shall die upon trying to claim it.'

Naruto just stepped back for a second and mentally asked his half of Kurama, 'Is this for real?'

Yang Kurama answered, "Yes. It is true. This is my father's staff. Take it, boy. You have his eyes and his heart. With its power, all elemental releases will be yours to use.

Naruto grabbed hold of the staff's handle and the stone base glowed white as he pulled it free. A bright white light fired from the stone base through the temple roof and high into the sky, signalling that a new Sage of the Six Paths had arrived.

Naruto paid no mind to the lightshow as he looked at the staff. It had seven rings, each with an elemental symbol. He could only guess they were used to store chakra of that element to combine them.

Naruto chose to test it by focusing chakra into the water and wind rings and holding the staff out towards the wall. In a second, from the staff fired a beam of ice that froze the wall solid. Naruto had just used Ice Release.

Naruto smiled as he turned around and walked away, tapping the staff on the ground with each step.

Meanwhile, with Shinji…

He and his Naruto clone partner came to a tower in the middle of the ruined village and, once Shinji saw it, a silhouette of Eva-01 appeared and under it was writing.

Shinji's eyes widened as he began to read. "From another world, a fox of darkness shall come, sent here by his mother to keep him safe from his wicked father and with him shall be a monster made by the hands of man to be a beast of war."

The Naruto clone turned around and looked at the tower wall so that the original and other three clones could see it. "It's talking about you, Shinji," said the clone.

Shinji didn't listen to the Naruto clone and simply continued. "This beast had a home in the fox of darkness's homeland and shall be summoned by the fox in his greatest hours of need and, with the titan's arrival, someone new will arrive to guide the fox to the right path."

That was where it stopped. The rest of this prophecy was lost with the rest of the tower and to history.

As if Shinji's day wasn't made weird enough by this find, he soon started to see through the eyes of the Evangelion once more. But, unlike the last time, it was different he could feel someone inside Eva-01.

Meanwhile, in NERV…

It was morning and Rei was inside Eva-01 as Gendo asked her to try to synch with it; something everyone was against.

Hikari looked at the monster that she just learned took Shinji away. "How could they put someone else in that thing after what it did to Shinji?"

Asuka just crossed her arms. "Who cares what happened to the little man-bitch?"

Hikari rolled her eyes. She used to think that Asuka was a good person, but now that she was seeing her at NERV being her real self, she soon found out what a motherfucking bitch she was.

Maya was working at her computer when the screen showed two other minds appearing on Rei's synchronization test and she screamed, "IT'S HAPPENING AGAIN!"

With Rei…

She began to synch so deep with Eva-01 that she found herself in a sewer.

Rei soon heard Shinji's voice saying, "Follow me, Rei!"

Rei jumped and turned around to see Shinji in his new outfit, proudly making sure that his headband shone. Shinji seemed more confidant and stronger of mind… It was unnerving, to say the least.

Shinji looked at her and crossed his arms. "Rei, I know you're a half-Angel clone of my mom." Rei gasped once. But, before she could say anything, Shinji said, "But, since you were born of my mom and made by Gendo, that kind of makes us brother and sister."

Rei was stunned beyond all reason.

Shinji grabbed her hand, pulled her along and said, "We're not in the Evangelion anymore, Rei. We are in the darkest corner of my mind. And also I'm not in side unite one my mind is just linked to it."

Rei listened as Shinji pulled her along, so she only asked, "So, then, where are you?"

Shinji responded, "In another world where people have learned how to use the AT Field, but they call it chakra. Anyway, they use it for everything and it has replaced technology, so it's like feudal Japan but everyone has super powers."

Rei listened on. Shinji showed no sign of lying, so she asked, "What of their Angels?"

Shinji stopped at a large cage and let go of her hand. "Well, little sis, they have demons – not Angels – all born form one real big ass demon that some Sage stood up to and ripped into nine pieces."

Rei blinked for three reasons. First, Shinji called her his little sister which made her feel what she could only guess was happiness. Second, he said a bad word. Third, a monk ripped an Angel into nine parts.

Shinji continued. "Each piece of it became its own demon which the Sage sealed by locking them within his own soul. But, when he died, the demons were set free so nine families each sealed them within one of their own. The job of the demon's jailer is past down from parent to child."

Rei looked to the cage. "What's the cage for?"

Shinji spoke. "Simple. Now, the demons have very powerful chakra to the point that you can gather a large amount of it by going somewhere they travelled through and then putting that into someone. But, demon number nine, the strongest, was split in two when it was sealed last."

Rei, still not putting things together, asked again, "What does that have to do with the cage?"

"When a demon, or Tailed Beast, as they are called, die, they reform after years and the other half of number nine reformed when I arrived, so, Rei, let me introduce you to the evil half of the Nine Tailed Demon Fox, Yin Kurama."

From within the cage, Rei saw two giant red eyes that broke all the barriers around Rei's emotions in a second and filled her with fear.

Soon a mouth opened showing a giant set of devilish teeth as an evil voice said, "I see we have a guest!"

Rei backed away as three more things clicked in her mind. Shinji was her brother, demons were real and one of them was living inside of her brother.

Rei fell down in fear.

Shinji walked over to her and helped her up. "Relax, sis. He can't leave his cage and the only danger you have to worry about is that he starts to take over when I get mad."

Rei stood up. She was still shaking. The eyes of this demon behind the bars of the cage would forever haunt her, for when she looked into them, she saw the same kind of eyes that Gendo had. The eyes of a devil.

Shinji looked at her and gave her a hug. "I'm sorry, Rei, but I have to go now because, while this is going on, I'm standing outside like a statue in the real world and it's not a good idea since everyone there has super powers."

Rei then opened her eyes to find herself in Eva-01 holding herself as she shook with fear and thought, 'Those eyes were like Gendo's and if Gendo has the eyes of a demon then he is one. Demons are evil, so Gendo is evil and evil must be stopped.'

Back with Shinji…

He started rubbing his eyes as the Naruto clone asked, "The link to that purple beast again?"

Shinji nodded 'yes' as he hoped that Rei would be ok.

Time passed and it turned out that the only thing left in the village was the Sage's staff.

Anko sighed. "All day and we only got one weapon. What a waste of a day."

Naruto smirked. "I think I can change that, Anko. You see, the Nine Tailed Fox was locked away here for one and a half generations, so a lot of its chakra is here, and with my power to absorb chakra, I think I can use it for something grand."

Jiraiya simply hid behind a rock, knowing were his student was going.

Yamato simply said, "I know what you're going to do."

Naruto raised his hand. Red chakra pulled itself from all over the ruined village and formed in his hand. The chakra soon took the shape of a fox with three tails, no bigger than Akamaru.

The mass of chakra soon became an Akamaru-sized three-tailed baby fox demon that yipped to life.

Anko fainted.

Hinata picked up the little thing, throwing him in the air and catching him as she yelled, "KKKAAAWWAAIIII!"

Shinji looked on and simply said one thing. "What the hell is going on with my life?"

To be continued…


	8. HFASSSOTLpart 3 seaNerv's true mission

Naruto's group we're on a ferry On to one of the islands of the land of the sea.

Naruto was sitting on the ground with his arms crossed, "Why are we heading to the land of The sea again?"

Anko looked at him, "While that's simple ring eyes, This was the last place I saw Orochimaru when he was still a shinobi of the leaf, plus with all the people disappearing around here it looks like the bastard is kidnapping people to use in his sick twisted experiments."

Naruto just rolled his eyes at the nickname as he used Creation of all things to make a pair of sun glasses to hide the Rinnegan.

Shinji looked over to Naruto and said, "Lighten up Naruto, If the snake is here then your sister might be here to."

Naruto just put on the sun glasses as Hinata blushed and grabbed on to his hand, Making the Rinnegan user smile a little.

Yamato looked at Naruto and said, "After this phase of the mission we will begin your training in using wood release Naruto."

Once more Naruto nodded along.

Jiraiya looked At Shinji, "and I'll have you sign the toad contract Shinji."

Shinji nodded yes and said, "yes pervy sage sensei." The self proclaimed super pervert just growled at the name.

Meanwhile a world away Rei was in her apartment sitting on her bed thinking of what happened today.

Rei had her hand on her chin, "Demons are suppose to be evil. But Angels are suppose to be good yet the angels we pilots battle are evil. So if an angel can be evil, A demon can be good then."

The now semi-emotionless girl laid down on her bed and thought out loud, "Should I even share any of this with anyone? And if I did would they believe it?"

Rei then heard a knock on her door and got up as she thought aloud, "If I told anyone they would probably lock me up and throw away the key."

Rei opened the door to see a shaking Captain Misato Katsuragi.

The shaking Captain grabbed Rei by the shirt and starting shaking the half angel. "YOU SPOKE WITH SHINJI TELL ME WHAT HAPPENED AND WHY HE ISN'T COMING OUT NOW!"

Rei was dizzy form the shaking but she was able to say "Stop shaking me and I'll tell you but you probably won't believe it."

Misato stopped shaking her and so began a night of shocking truths.

Rei told Misato everything Shinji told her, and about what Nerv's real mission is.

To say the lest Misato was shocked but seeing as Rei was to unemotional to lie, she knew every last word was true. She thought she was helping stop the angels but no she was helping kill all of humanity.

Rei put her hand on her heart and looked down. "I hope you don't think less of me for going along with this, or That I'm half angel. I saw Gendo as my creator and the only family I had. But I know better now Shinji is my brother and he cares about me so I now side with him only."

Misato was watching Rei show emotion, that had to be a sign the end was near. "I don't think less of you Rei After all if your Shinji's sister, and I can't bring myself to hate anyone Shinji cares about."

Rei looked at her for a second before asking. "you want to fuck my brother don't you captain?"

Misato jumped back and yelled "WHAT THE HELL!"

Rei crossed her arms, "it's written in your face, and your clearly not phased by the demon in him."

Misato held her heart " because I had a nightmare of Shinji turning into a monster, I thought it was crazy. But no I know if he gets mad that's what the demon will turn him into. And His the only nice guy I've ever had in my life if the age difference wasn't so high I would jump him"

Rei looked at her " you know in four years he'll be 18 right?"

Misato blushed, "ok you got me I was planning on jumping him on his 18 birthday if his still signal. Happy now miss angel?"

Rei nodded yes and said, "now what do we do about Nerv with out Shinji?"

To be continued.


End file.
